The Philippine military is under new pressure after a government-backed commission linked some soldiers to a spate of political killings.
Hundreds of activists have been killed, rights groups say
The commission's report came a day after a UN envoy accused the army of being in "denial" over the issue of extra-judicial killings.
A rights group said 830 activists had been killed since President Gloria Arroyo came to power in 2001.
Ms Arroyo said she would take the findings and allegations seriously.
"The government is not in denial, these killings will be resolved and the armed forces shall continue to be a vanguard of freedom," she said in a statement.
The head of the armed forces, General Hermogenes Esperon, hit back at the criticism.
He said he thought the UN envoy, Philip Alston, "might be in a state of denial himself", criticising him for ignoring evidence of alleged assassinations by Communist rebels.
Gen Esperon described the findings of the latest report as "strained, unfair and a blank accusation".
The report by the government-backed inquiry, headed by retired Philippine judge Jose Melo, found "elements in the military" were responsible for the deaths of some activists.
"To maintain otherwise would be closing one's eyes to reality," the Melo Report said.
Philip Alston presented his provisional findings in Manila
Presidential spokesman Ignacio Bunye said Ms Arroyo believed that the majority of soldiers were not involved.
"We know that most members of the Armed Forces are doing their job. But there are some bad eggs. We all recognize that we have a problem," he said, according to local media.
Like Mr Alston, the report found no evidence that the killings had been politically sanctioned.
But the report said there was evidence the army's former head of counter-insurgency, General Jovito Palparan, and others were implicated in some of the killings.
"General Palparan and perhaps some of his superior officers may be held responsible for failing to prevent, punish or condemn the killings under the principle of command responsibility," the report said.
General Palparan has denied any wrongdoing.
Human rights group Karapatan says the 832 extra-judicial killings recorded since 2001 can be blamed on the security forces. Of these, it says 356 were left-wing activists.
The Philippines armed forces have been fighting a Communist insurgency since 1969, in which an estimated 40,000 people have been killed. More recently troops have also had to face attacks by Muslim radicals.